Solvent structure at a hydrophobic protein surface

Kovacs, Helena; Mark, Alan E.; Gunsteren, Wilfred F. van

doi:10.1002/(sici)1097-0134(199703)27:3<395::aid-prot7>3.0.co;2-c

Cited by 45 publications

(44 citation statements)

References 33 publications

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“…In harmony with the present work, in several recent studies (35)(36)(37) no clear relationship between first-shell water density variations and the hydrophobicity͞hydrophilicity of chemical groups has been found. Moreover, in the present simulation, although the water oxygen:surface protein atom PCFs in Fig.…”

Section: Discussionsupporting

confidence: 89%

Is the first hydration shell of lysozyme of higher density than bulk water?

Merzel

Smith²

2002

Proc. Natl. Acad. Sci. U.S.A.

356

276

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Characterization of the physical properties of protein surface hydration water is critical for understanding protein structure and folding. Here, using molecular dynamics simulation, we provide an explanation of recent x-ray and neutron solution scattering data that indicate that the density of water on the surface of lysozyme is significantly higher than that of bulk water. The simulationderived scattering profiles are in excellent agreement with the experiment. In the simulation, the 3-Å-thick first hydration layer is 15% denser than bulk water. About two-thirds of this increase is the result of a geometric contribution that would also be present if the water was unperturbed from the bulk. The remaining third arises from modification of the water structure and dynamics, involving approximately equal contributions from shortening of the average water-water O-O distance and an increase in the coordination number. Variation in the first hydration shell density is shown to be determined by topographical and electrostatic properties of the protein surface. On average, denser water is found in depressions on the surface in which the water dipoles tend to be aligned parallel to each other by the electrostatic field generated by the protein atoms.A characterization of protein hydration is essential for understanding protein structure, folding, and function. This characterization requires elucidating the effects of both the solvent on the protein and the protein on the solvent (1, 2). Concerning the latter effect, detailed information on ordering and dynamical properties of individual, highly perturbed, strongly bound water molecules has been furnished by highresolution x-ray crystallography and NMR spectroscopy (3-10). However, to obtain the data required for a complete thermodynamic description of protein hydration it is necessary to obtain a more global picture in which the solvent is described in terms of probability distributions. Recent work in this direction has used molecular dynamics (MD) simulation (11-13) and novel crystallographic methods (6,7,14) to enable radial distribution functions of water molecules around protein groups in crystals and related quantities to be obtained.It is of particular importance to determine how protein surface water is on average perturbed from the bulk. An intriguing result in this regard was reported by Svergun et al. (15), who combined small-angle scattering (SAS) of x-rays in H 2 O with that of neutrons in H 2 O and D 2 O to show that for lysozyme and other proteins the average density of the first hydration shell (0-3 Å from the surface) is significantly higher than that of bulk water. This finding is consistent with results from MD simulation (16) and the crystallographic work (14). The present article explains the physical origin of this effect. We use MD simulation of lysozyme in explicit water to determine the contributions to the hydration density profile. The MD allows detailed structural properties of the hydration water to be analyzed in the context of the SAS resul...

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Section: Discussionsupporting

confidence: 89%

Is the first hydration shell of lysozyme of higher density than bulk water?

Merzel

Smith²

2002

Proc. Natl. Acad. Sci. U.S.A.

356

276

View full text Add to dashboard Cite

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“…B (2004) shell water density and the chemical characteristics of the surface atoms or residues, for example, whether polar/non-polar or hydrophobic/hydrophilic. In agreement with this result, in several recent studies (Finney et al 1993;Pertsemlidis et al 1996;Kovacs et al 1997) no clear relationship between first-shell water density variations and the hydrophobicity/hydrophilicity of chemical groups has been found. The exceptions are groups with net charges, about which the density is increased.…”

Section: Solvent Structure On a Protein Surfacesupporting

confidence: 71%

Structure, dynamics and reactions of protein hydration water

Smith

Merzel

Bondar

et al. 2004

Phil. Trans. R. Soc. Lond. B

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The apparent simplicity of the water molecule belies the wide range of fascinating protein phenomena in which it participates. We review recent computer simulation work on buried, internal water molecules, discussing the thermodynamics of water molecule binding and the participation of water in proton transfer reactions. Surface water molecules are also considered, with emphasis on the modification of average solvent structure on a protein surface, the role of water in the protein dynamical 'glass' transition and a simplified description of the protein motions thereby activated.

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“…NMR and neutron spectroscopy have revealed altered mobility of water molecules on protein surfaces with respect to the bulk (11)(12)(13)(14)(15), and time-resolved vibrational spectroscopy has revealed distinctive dynamics of solvation near the active sites of enzymes during catalysis with respect to bulk solvent (16). Increased water density in the first hydration shell (HS), as well as surface-specific differences in the organization of the hydration water, have been reported by MD simulations (17)(18)(19)(20) and have been described thermodynamically in terms of electrorestriction (21). MD studies involving nucleic acids (7,22,23) or proteins (24,25), as well as anomalous x-ray solution studies on proteins and nucleic acids (26,27), have revealed the specific recruitment of ions into their HSs.…”

Section: Introductionmentioning

confidence: 95%

SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell

Kim

Martel

Girard

et al. 2016

Biophysical Journal

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Water molecules in the immediate vicinity of biomacromolecules, including proteins, constitute a hydration layer characterized by physicochemical properties different from those of bulk water and play a vital role in the activity and stability of these structures, as well as in intermolecular interactions. Previous studies using solution scattering, crystallography, and molecular dynamics simulations have provided valuable information about the properties of these hydration shells, including modifications in density and ionic concentration. Small-angle scattering of x-rays (SAXS) and neutrons (SANS) are particularly useful and complementary techniques to study biomacromolecular hydration shells due to their sensitivity to electronic and nuclear scattering-length density fluctuations, respectively. Although several sophisticated SAXS/SANS programs have been developed recently, the impact of physicochemical surface properties on the hydration layer remains controversial, and systematic experimental data from individual biomacromolecular systems are scarce. Here, we address the impact of physicochemical surface properties on the hydration shell by a systematic SAXS/SANS study using three mutants of a single protein, green fluorescent protein (GFP), with highly variable net charge (þ36, À6, and À29). The combined analysis of our data shows that the hydration shell is locally denser in the vicinity of acidic surface residues, whereas basic and hydrophilic/hydrophobic residues only mildly modify its density. Moreover, the data demonstrate that the density modifications result from the combined effect of residue-specific recruitment of ions from the bulk in combination with water structural rearrangements in their vicinity. Finally, we find that the specific surface-charge distributions of the different GFP mutants modulate the conformational space of flexible parts of the protein.

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Solvent structure at a hydrophobic protein surface

Cited by 45 publications

References 33 publications

Is the first hydration shell of lysozyme of higher density than bulk water?

Is the first hydration shell of lysozyme of higher density than bulk water?

Structure, dynamics and reactions of protein hydration water

SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell

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